MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000533902
Querying Taster for transcript #2: ENST00000531380
MT speed 0 s - this script 5.762418 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FZD4	disease_causing_automatic	0.999996907727476	simple_aae			0	M342V	single base exchange	rs80358293		show file
PRSS23	disease_causing_automatic	1	without_aae			0		single base exchange	rs80358293		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999996907727476 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM042704)
known disease mutation: rs5487 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:86662774T>CN/A show variant in all transcripts IGV

HGNC symbol

FZD4

Ensembl transcript ID

ENST00000531380

Genbank transcript ID

NM_012193

UniProt peptide

Q9ULV1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1024A>G
cDNA.1330A>G
g.3660A>G

AA changes

M342V Score: 21 explain score(s)

position(s) of altered AA
if AA alteration in CDS

342

frameshift

known variant

Reference ID: rs80358293

database	homozygous (C/C)	heterozygous	allele carriers
1000G	0	1	1
ExAC	-	-	-

known disease mutation: rs5487 (pathogenic for Exudative vitreoretinopathy 1) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042704)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042704)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042704)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.57	1
	3.463	1
(flanking)	0.547	0.998

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	3654	wt: 0.9421 / mu: 0.9931 (marginal change - not scored)	wt: AAGCCATTGAAATGC mu: AAGCCATTGAAGTGC	GCCA\|ttga

distance from splice site

739

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

342

mutated

all conserved

342

Ptroglodytes

all identical

ENSPTRG00000004148

342

Mmulatta

all identical

ENSMMUG00000004048

342

Fcatus

all identical

ENSFCAG00000011826

345

Mmusculus

all identical

ENSMUSG00000049791

342

Ggallus

all identical

ENSGALG00000017242

330

Trubripes

all identical

ENSTRUG00000006345

334

Drerio

all identical

ENSDARG00000077111

329

Dmelanogaster

not conserved

FBgn0016797

435

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000010434

328

protein features

start (aa)	end (aa)	feature	details
324	344	TOPO_DOM	Cytoplasmic (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1614 / 1614

position (AA) of stopcodon in wt / mu AA sequence

538 / 538

position of stopcodon in wt / mu cDNA

1920 / 1920

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

307 / 307

chromosome

strand

-1

last intron/exon boundary

592

theoretical NMD boundary in CDS

235

length of CDS

1614

coding sequence (CDS) position

1024

cDNA position
(for ins/del: last normal base / first normal base)

1330

gDNA position
(for ins/del: last normal base / first normal base)

3660

chromosomal position
(for ins/del: last normal base / first normal base)

86662774

original gDNA sequence snippet

GGGGTCATGAAGCCATTGAAATGCACAGCTCTTATTTCCAC

altered gDNA sequence snippet

GGGGTCATGAAGCCATTGAAGTGCACAGCTCTTATTTCCAC

original cDNA sequence snippet

GGGGTCATGAAGCCATTGAAATGCACAGCTCTTATTTCCAC

altered cDNA sequence snippet

GGGGTCATGAAGCCATTGAAGTGCACAGCTCTTATTTCCAC

wildtype AA sequence

MAWRGAGPSV PGAPGGVGLS LGLLLQLLLL LGPARGFGDE EERRCDPIRI SMCQNLGYNV
TKMPNLVGHE LQTDAELQLT TFTPLIQYGC SSQLQFFLCS VYVPMCTEKI NIPIGPCGGM
CLSVKRRCEP VLKEFGFAWP ESLNCSKFPP QNDHNHMCME GPGDEEVPLP HKTPIQPGEE
CHSVGTNSDQ YIWVKRSLNC VLKCGYDAGL YSRSAKEFTD IWMAVWASLC FISTAFTVLT
FLIDSSRFSY PERPIIFLSM CYNIYSIAYI VRLTVGRERI SCDFEEAAEP VLIQEGLKNT
GCAIIFLLMY FFGMASSIWW VILTLTWFLA AGLKWGHEAI EMHSSYFHIA AWAIPAVKTI
VILIMRLVDA DELTGLCYVG NQNLDALTGF VVAPLFTYLV IGTLFIAAGL VALFKIRSNL
QKDGTKTDKL ERLMVKIGVF SVLYTVPATC VIACYFYEIS NWALFRYSAD DSNMAVEMLK
IFMSLLVGIT SGMWIWSAKT LHTWQKCSNR LVNSGKVKRE KRGNGWVKPG KGSETVV*

mutated AA sequence

MAWRGAGPSV PGAPGGVGLS LGLLLQLLLL LGPARGFGDE EERRCDPIRI SMCQNLGYNV
TKMPNLVGHE LQTDAELQLT TFTPLIQYGC SSQLQFFLCS VYVPMCTEKI NIPIGPCGGM
CLSVKRRCEP VLKEFGFAWP ESLNCSKFPP QNDHNHMCME GPGDEEVPLP HKTPIQPGEE
CHSVGTNSDQ YIWVKRSLNC VLKCGYDAGL YSRSAKEFTD IWMAVWASLC FISTAFTVLT
FLIDSSRFSY PERPIIFLSM CYNIYSIAYI VRLTVGRERI SCDFEEAAEP VLIQEGLKNT
GCAIIFLLMY FFGMASSIWW VILTLTWFLA AGLKWGHEAI EVHSSYFHIA AWAIPAVKTI
VILIMRLVDA DELTGLCYVG NQNLDALTGF VVAPLFTYLV IGTLFIAAGL VALFKIRSNL
QKDGTKTDKL ERLMVKIGVF SVLYTVPATC VIACYFYEIS NWALFRYSAD DSNMAVEMLK
IFMSLLVGIT SGMWIWSAKT LHTWQKCSNR LVNSGKVKRE KRGNGWVKPG KGSETVV*

speed

1.42 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM042704)
known disease mutation: rs5487 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:86662774T>CN/A show variant in all transcripts IGV

HGNC symbol

PRSS23

Ensembl transcript ID

ENST00000533902

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

3'UTR

DNA changes

cDNA.865T>C
g.160674T>C

AA changes

N/A

position(s) of altered AA
if AA alteration in CDS

N/A

frameshift

N/A

known variant

Reference ID: rs80358293

database	homozygous (C/C)	heterozygous	allele carriers
1000G	0	1	1
ExAC	-	-	-

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.57	1
	3.463	1
(flanking)	0.547	0.998

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	160665	wt: 0.9766 / mu: 0.9856 (marginal change - not scored)	wt: ATAAGAGCTGTGCAT mu: ATAAGAGCTGTGCAC	AAGA\|gctg

distance from splice site

517

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

position (AA) of stopcodon in wt / mu AA sequence

N/A

position of stopcodon in wt / mu cDNA

N/A

poly(A) signal

signal is predicted to be ok

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

143 / 143

chromosome

strand

last intron/exon boundary

349

theoretical NMD boundary in CDS

156

length of CDS

276

coding sequence (CDS) position

N/A

cDNA position
(for ins/del: last normal base / first normal base)

865

gDNA position
(for ins/del: last normal base / first normal base)

160674

chromosomal position
(for ins/del: last normal base / first normal base)

86662774

original gDNA sequence snippet

GTGGAAATAAGAGCTGTGCATTTCAATGGCTTCATGACCCC

altered gDNA sequence snippet

GTGGAAATAAGAGCTGTGCACTTCAATGGCTTCATGACCCC

original cDNA sequence snippet

GTGGAAATAAGAGCTGTGCATTTCAATGGCTTCATGACCCC

altered cDNA sequence snippet

GTGGAAATAAGAGCTGTGCACTTCAATGGCTTCATGACCCC

wildtype AA sequence

MSRMRPVCQP WPSPHAPTTV KREGSTVSNS IQPPPPEYQL GSRTWLEAET PGQKRQCSAF
MEFTEESRRI HQSVGTLLPR VKSFGRPNPH A*

mutated AA sequence

N/A

speed

1.42 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems